Rmarkdown

# Rmarkdown
## The first trick
### Fabio CRUZ
### Université de Lorraine
### 2021/02/01 (updated: 2021-01-29)

---

# We are assuming...

You have know how works:
- Github
- RStudio

And you are eager to see the magic happen.

So let's start...

```{=html}
<div class="countdown" id="timer_60147342" style="right:0;bottom:0;left:0;margin:5%;padding:15px;font-size:6em;" data-warnwhen="0">
<code class="countdown-time"><span class="countdown-digits minutes">01</span><span class="countdown-digits colon">:</span><span class="countdown-digits seconds">30</span></code>
</div>
```

---

# Learning outcomes

- You will produce your first reproducible document and put it online 
- You will have a basic understanding of the main functions of Rmarkdown

---

# Agenda of this sprint

### 1. Understanding the Rmarkdown

### 2. Connecting with github to publish your work!

---

# What is Rmarkdown?

---
background-image: url(data:image/png;base64,#img/screenshots/Single-rmd.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

**here**, you can see a typical single R Markdown file. <br>
This one is for a lab for visualizing data from the Museum of Modern Art.<br>
Let's quickly walk through some of the key parts of this file.

---
background-image: url(data:image/png;base64,#img/screenshots/Single-rmd0.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

It starts with **metadata**, written in `YAML`, which is a list of keys on the left and their values on the right.

---
background-image: url(data:image/png;base64,#img/screenshots/Single-rmd1.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

The first key you see is the **TITLE**, which is `Lab 02: MoMA Museum Tour`.

---
background-image: url(data:image/png;base64,#img/screenshots/Single-rmd2.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

The last YAML section is all about **output**. Here the output is an **`html_document`**.
---
background-image: url(data:image/png;base64,#img/screenshots/Single-rmd3.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

Beneath that, we can add options to our **`html_document`** 
  - for example, a table of contents, with the key **TOC** set to **TRUE**.

---
background-image: url(data:image/png;base64,#img/screenshots/Single-rmd4.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

So that's the metadata, but the real meat in your R Markdown file 
is text written in **markdown**...

---
Markdown

---
background-image: url(data:image/png;base64,#img/screenshots/Single-rmd5.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

and your code, written in R. So these 3 things: (1) **Metadata**, (2) *Text*, and (3) **Code** make up an *R Markdown* document.

---

The real magic happens, when you click on the `**Knit icon**`, and see your file turned into HTML.

---

background-image: url(data:image/png;base64,#img/screenshots/Single-knit1.png)
background-position: 50% 5px
background-size: 70%
class: middle, bottom

Here is what we knit.

Using the **`THEME:`** key in our YAML, we changed our font and colors.

But **this is still local and stuck on my computer/ Rstudio Cloud**.

---
name: clouds
class: center, middle
background-image: url(data:image/png;base64,#img/Clouds.jpg)
background-size: cover

# How do we start .emphasis[sharing]?

# We are going to publish this on the web !

---

# Commit your files on github

1. Go to the `Environment Panel`and got to `Git` tab.

2. Select each element that appears to be changed.
  - You can use `Ctrl / Cmd + A` to select of of them, and press `Enter`

3. Click on Commit

4. Click on `Push`